+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9674 | |||||||||
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Title | Cryo-EM structure of CV-A10 mature virion | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Coxsackievirus A10 / Mature virion / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information symbiont genome entry into host cell via pore formation in plasma membrane / symbiont-mediated suppression of host gene expression / viral capsid / virion attachment to host cell / structural molecule activity Similarity search - Function | |||||||||
Biological species | Coxsackievirus A10 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.84 Å | |||||||||
Authors | Chen JH / Ye XH | |||||||||
Citation | Journal: Cell Discov / Year: 2019 Title: Coxsackievirus A10 atomic structure facilitating the discovery of a broad-spectrum inhibitor against human enteroviruses. Authors: Jinhuan Chen / Xiaohua Ye / Xue-Yang Zhang / Zhengdan Zhu / Xiang Zhang / Zhijian Xu / Zhanyu Ding / Gang Zou / Qingwei Liu / Liangliang Kong / Wen Jiang / Weiliang Zhu / Yao Cong / Zhong Huang / Abstract: Coxsackievirus A10 (CV-A10) belongs to the species A and is a causative agent of hand, foot, and mouth disease. Here we present cryo-EM structures of CV-A10 mature virion and native empty particle ...Coxsackievirus A10 (CV-A10) belongs to the species A and is a causative agent of hand, foot, and mouth disease. Here we present cryo-EM structures of CV-A10 mature virion and native empty particle (NEP) at 2.84 and 3.12 Å, respectively. Our CV-A10 mature virion structure reveals a density corresponding to a lipidic pocket factor of 18 carbon atoms in the hydrophobic pocket formed within viral protein 1. By structure-guided high-throughput drug screening and subsequent verification in cell-based infection-inhibition assays, we identified four compounds that inhibited CV-A10 infection in vitro. These compounds represent a new class of anti-enteroviral drug leads. Notably, one of the compounds, ICA135, also exerted broad-spectrum inhibitory effects on a number of representative viruses from all four species (A-D) of human enteroviruses. Our findings should facilitate the development of broadly effective drugs and vaccines for enterovirus infections. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9674.map.gz | 41.3 MB | EMDB map data format | |
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Header (meta data) | emd-9674-v30.xml emd-9674.xml | 12.2 KB 12.2 KB | Display Display | EMDB header |
Images | emd_9674.png | 109.9 KB | ||
Filedesc metadata | emd-9674.cif.gz | 5.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9674 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9674 | HTTPS FTP |
-Related structure data
Related structure data | 6iijMC 9675C 6iioC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_9674.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.005 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Coxsackievirus A10
Entire | Name: Coxsackievirus A10 |
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Components |
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-Supramolecule #1: Coxsackievirus A10
Supramolecule | Name: Coxsackievirus A10 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / NCBI-ID: 42769 / Sci species name: Coxsackievirus A10 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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-Macromolecule #1: VP1
Macromolecule | Name: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Coxsackievirus A10 |
Molecular weight | Theoretical: 33.088219 KDa |
Sequence | String: GDPVEDIIHD ALGNTARRAI SGATNVESAA DTTPSSHRLE TGRVPALQAA ETGATSNATD ENMIETRCVI NRNGVLETTI NHFFSRSGL VGVVNLTDGG DTTGYATWDI DIMGFVQLRR KCEMFTYMRF NAEFTFVTTT KSGEARPYML QYMYVPPGAP K PTGRDAFQ ...String: GDPVEDIIHD ALGNTARRAI SGATNVESAA DTTPSSHRLE TGRVPALQAA ETGATSNATD ENMIETRCVI NRNGVLETTI NHFFSRSGL VGVVNLTDGG DTTGYATWDI DIMGFVQLRR KCEMFTYMRF NAEFTFVTTT KSGEARPYML QYMYVPPGAP K PTGRDAFQ WQTATNPSVF VKLTDPPAQV SVPFMSPASA YQWFYDGYPT FGQHPETSNT TYGLCPNNMM GTFAVRVVSR EA SQLKLQT RVYMKLKHVR AWVPRPIRSQ PYLLKNFPNY DSSKITNSAR DRSSIKQANM UniProtKB: Genome polyprotein |
-Macromolecule #2: VP2
Macromolecule | Name: VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Coxsackievirus A10 |
Molecular weight | Theoretical: 27.741023 KDa |
Sequence | String: SPSVEACGYS DRVAQLTVGN SSITTQEAAN IVLAYGEWPE YCPDTDATAV DKPTRPDVSV NRFYTLDSKM WQENSTGWYW KFPDVLNKT GVFGQNAQFH YLYRSGFCLH VQCNASKFHQ GALLVAVIPE FVIAGRGSNT KPNEAPHPGF TTTFPGTTGA T FHDPYVLD ...String: SPSVEACGYS DRVAQLTVGN SSITTQEAAN IVLAYGEWPE YCPDTDATAV DKPTRPDVSV NRFYTLDSKM WQENSTGWYW KFPDVLNKT GVFGQNAQFH YLYRSGFCLH VQCNASKFHQ GALLVAVIPE FVIAGRGSNT KPNEAPHPGF TTTFPGTTGA T FHDPYVLD SGVPLSQALI YPHQWVNLRT NNCATVIVPY INAVPFDSAI NHSNFGLVVV PVSPLKYSSG ATTAIPITIT IA PLNSEFG GLRQAVSQ UniProtKB: Genome polyprotein |
-Macromolecule #3: VP3
Macromolecule | Name: VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Coxsackievirus A10 |
Molecular weight | Theoretical: 26.187623 KDa |
Sequence | String: GIPAELRPGT NQFLTTDDDT AAPILPGFTP TPTIHIPGEV HSLLELCRVE TILEVNNTTE ATGLTRLLIP VSSQNKADEL CAAFMVDPG RIGPWQSTLV GQICRYYTQW SGSLKVTFMF TGSFMATGKM LVAYSPPGSA QPANRETAML GTHVIWDFGL Q SSVSLVIP ...String: GIPAELRPGT NQFLTTDDDT AAPILPGFTP TPTIHIPGEV HSLLELCRVE TILEVNNTTE ATGLTRLLIP VSSQNKADEL CAAFMVDPG RIGPWQSTLV GQICRYYTQW SGSLKVTFMF TGSFMATGKM LVAYSPPGSA QPANRETAML GTHVIWDFGL Q SSVSLVIP WISNTHFRTA KTGGNYDYYT AGVVTLWYQT NYVVPPETPG EAYIIAMGAA QDNFTLKICK DTDEVTQQAV LQ UniProtKB: Genome polyprotein |
-Macromolecule #4: VP4
Macromolecule | Name: VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Coxsackievirus A10 |
Molecular weight | Theoretical: 7.464104 KDa |
Sequence | String: MGAQVSTQKS GSHETGNVAT GGSTINFTNI NYYKDSYAAS ATRQDFTQDP KKFTQPVLDS IRELSAPLN UniProtKB: Genome polyprotein |
-Macromolecule #5: SPHINGOSINE
Macromolecule | Name: SPHINGOSINE / type: ligand / ID: 5 / Number of copies: 1 / Formula: SPH |
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Molecular weight | Theoretical: 299.492 Da |
Chemical component information | ChemComp-SPH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: NITROGEN |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 8.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 13273 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |